Interventions to improve latent and active tuberculosis treatment completion rates in underserved groups in low incidence countries: a scoping review.

BACKGROUND: People in underserved groups have higher rates of tuberculosis (TB) and poorer treatment outcomes compared with people with no social risk factors. OBJECTIVES: This scoping review aimed to identify interventions that improve TB treatment adherence or completion rates. ELIGIBILITY CRITERIA: Studies of any design focusing on interventions to improve adherence or completion of TB treatment in underserved populations in low incidence countries. SOURCES OF EVIDENCE: MEDLINE, Embase and Cochrane CENTRAL were searched (January 2015 to December 2023). CHARTING METHODS: Piloted data extraction forms were used. Findings were tabulated and reported narratively. Formal risk of bias assessment or synthesis was not undertaken. RESULTS: 47 studies were identified. There was substantial heterogeneity in study design, population, intervention components, usual care and definition of completion rates. Most studies were in migrants or refugees, with fewer in populations with other risk factors (eg, homelessness, imprisonment or substance abuse). Based on controlled studies, there was limited evidence to suggest that shorter treatment regimens, video-observed therapy (compared with directly observed therapy), directly observed therapy (compared with self-administered treatment) and approaches that include tailored health or social support beyond TB treatment may lead to improved outcomes. This evidence is mostly observational and subject to confounding. There were no studies in Gypsy, Roma and Traveller populations, or individuals with mental health disorders and only one in sex workers. Barriers to treatment adherence included a lack of knowledge around TB, lack of general health or social support and side effects. Facilitators included health education, trusted relationships between patients and healthcare staff, social support and reduced treatment duration. CONCLUSIONS: The evidence base is limited, and few controlled studies exist. Further high-quality research in well-defined underserved populations is needed to confirm the limited findings and inform policy and practice in TB management. Further qualitative research should include more people from underserved groups.

Computational prediction of MHC anchor locations guides neoantigen identification and prioritization.

Neoantigens are tumor-specific peptide sequences resulting from sources such as somatic DNA mutations. Upon loading onto major histocompatibility complex (MHC) molecules, they can trigger recognition by T cells. Accurate neoantigen identification is thus critical for both designing cancer vaccines and predicting response to immunotherapies. Neoantigen identification and prioritization relies on correctly predicting whether the presenting peptide sequence can successfully induce an immune response. Because most somatic mutations are single-nucleotide variants, changes between wild-type and mutated peptides are typically subtle and require cautious interpretation. A potentially underappreciated variable in neoantigen prediction pipelines is the mutation position within the peptide relative to its anchor positions for the patient's specific MHC molecules. Whereas a subset of peptide positions are presented to the T cell receptor for recognition, others are responsible for anchoring to the MHC, making these positional considerations critical for predicting T cell responses. We computationally predicted anchor positions for different peptide lengths for 328 common HLA alleles and identified unique anchoring patterns among them. Analysis of 923 tumor samples shows that 6 to 38% of neoantigen candidates are potentially misclassified and can be rescued using allele-specific knowledge of anchor positions. A subset of anchor results were orthogonally validated using protein crystallography structures. Representative anchor trends were experimentally validated using peptide-MHC stability assays and competition binding assays. By incorporating our anchor prediction results into neoantigen prediction pipelines, we hope to formalize, streamline, and improve the identification process for relevant clinical studies.

Understanding the factors influencing implementation of a new national patient safety policy in England: Lessons from 'learning from deaths'.

OBJECTIVE: A new patient safety policy, 'Learning from Deaths' (LfD), was implemented in 2017 in National Health Service (NHS) organisations in England. This study examined how contextual factors influenced the implementation of LfD policy and the ability of the programme to achieve its goals. METHODS: Semi-structured interviews were undertaken with key policymakers involved in the development of the policy, along with interviews with managers and senior clinicians in five NHS organisations responsible for implementing the policy at the local level. We also undertook non-participant observation of relevant meetings and documentary reviews of key organisation procedures and policies pertaining to LfD. RESULTS: The study findings suggest several factors that hinder or support patient safety policy implementation at a local level. These include: (a) an organisation's capacity and capability to support data collation, analysis and synthesis, (b) the dissemination of the resulting information, (c) the learning culture and hence perceptions of the purpose of LfD within an organisation, and (d) the extent of engagement in cross-organisational approaches to learning. CONCLUSIONS: Extra and intra-organisational contextual factors influence all stages of the policy implementation process from preparation and tracking to implementation support and review affecting its chances of success or failure. Successful adoption of a national patient safety policy within health care organisations can be informed by taking into consideration those factors.

In silico strategies to identify protein-protein interaction modulator in cell-to-cell transmission of SARS CoV2.

RNA sequence data from SARS CoV2 patients helps to construct a gene network related to this disease. A detailed analysis of the human host response to SARS CoV2 with expression profiling by high-throughput sequencing has been accomplished with primary human lung epithelial cell lines. Using this data, the clustered gene annotation and gene network construction are performed with the help of the String database. Among the four clusters identified, only 1 with 44 genes could be annotated. Interestingly, this corresponded to basal cells with p = 1.37e - 05, which is relevant for respiratory tract infection. Functional enrichment analysis of genes present in the gene network has been completed using the String database and the Network Analyst tool. Among three types of cell-cell communication, only the anchoring junction between the basal cell membrane and the basal lamina in the host cell is involved in the virus transmission. In this junction point, a hemidesmosome structure plays a vital role in virus spread from one cell to basal lamina in the respiratory tract. In this protein complex structure, different integrin protein molecules of the host cell are used to promote the spread of virus infection into the extracellular matrix. So, small molecular blockers of different anchoring junction proteins, such as integrin alpha 3, integrin beta 1, can provide efficient protection against this deadly viral disease. ORF8 from SARS CoV2 virus can interact with both integrin proteins of human host. By using molecular docking technique, a ternary complex of these three proteins is modelled. Several oligopeptides are predicted as modulators for this ternary complex. In silico analysis of these modulators is very important to develop novel therapeutics for the treatment of SARS CoV2.

Personalized ctDNA micro-panels can monitor and predict clinical outcomes for patients with triple-negative breast cancer.

Circulating tumor DNA (ctDNA) in peripheral blood has been used to predict prognosis and therapeutic response for triple-negative breast cancer (TNBC) patients. However, previous approaches typically use large comprehensive panels of genes commonly mutated across all breast cancers. Given the reduction in sequencing costs and decreased turnaround times associated with panel generation, the objective of this study was to assess the use of custom micro-panels for tracking disease and predicting clinical outcomes for patients with TNBC. Paired tumor-normal samples from patients with TNBC were obtained at diagnosis (T0) and whole exome sequencing (WES) was performed to identify somatic variants associated with individual tumors. Custom micro-panels of 4-6 variants were created for each individual enrolled in the study. Peripheral blood was obtained at baseline, during Cycle 1 Day 3, at time of surgery, and in 3-6 month intervals after surgery to assess variant allele fraction (VAF) at different timepoints during disease course. The VAF was compared to clinical outcomes to evaluate the ability of custom micro-panels to predict pathological response, disease-free intervals, and patient relapse. A cohort of 50 individuals were evaluated for up to 48 months post-diagnosis of TNBC. In total, there were 33 patients who did not achieve pathological complete response (pCR) and seven patients developed clinical relapse. For all patients who developed clinical relapse and had peripheral blood obtained ≤ 6 months prior to relapse (n = 4), the custom ctDNA micro-panels identified molecular relapse at an average of 4.3 months prior to clinical relapse. The custom ctDNA panel results were moderately associated with pCR such that during disease monitoring, only 11% of patients with pCR had a molecular relapse, whereas 47% of patients without pCR had a molecular relapse (Chi-Square; p-value = 0.10). In this study, we show that a custom micro-panel of 4-6 markers can be effectively used to predict outcomes and monitor remission for patients with TNBC. These custom micro-panels show high sensitivity for detecting molecular relapse in advance of clinical relapse. The use of these panels could improve patient outcomes through early detection of relapse with preemptive intervention prior to symptom onset.

Regulatory Roles of Noncoding RNAs in the Progression of Gastrointestinal Cancers and Health Disparities.

Annually, more than a million individuals are diagnosed with gastrointestinal (GI) cancers worldwide. With the advancements in radio- and chemotherapy and surgery, the survival rates for GI cancer patients have improved in recent years. However, the prognosis for advanced-stage GI cancers remains poor. Site-specific GI cancers share a few common risk factors; however, they are largely distinct in their etiologies and descriptive epidemiologic profiles. A large number of mutations or copy number changes associated with carcinogenesis are commonly found in noncoding DNA regions, which transcribe several noncoding RNAs (ncRNAs) that are implicated to regulate cancer initiation, metastasis, and drug resistance. In this review, we summarize the regulatory functions of ncRNAs in GI cancer development, progression, chemoresistance, and health disparities. We also highlight the potential roles of ncRNAs as therapeutic targets and biomarkers, mainly focusing on their ethnicity-/race-specific prognostic value, and discuss the prospects of genome-wide association studies (GWAS) to investigate the contribution of ncRNAs in GI tumorigenesis.

Efficacy of Individualized Homeopathic Medicines in the Treatment of Atopic Dermatitis in Adults: A Double-Blind, Randomized, Placebo-Controlled, Preliminary Trial.

INTRODUCTION: Individualized homeopathy (IH) in atopic dermatitis (AD) remained under-researched. OBJECTIVE: We aimed at evaluating efficacy of IH in AD. METHODS: A double-blind, randomized, placebo-controlled, short-term, preliminary trial was conducted in an Indian homeopathy hospital. Patients were randomized to either IH (n = 30) or identical-looking placebo (n = 30) using computerized randomization and allocation. Outcomes were patient-oriented scoring of AD (PO-SCORAD; primary end point), Dermatological Life Quality Index (DLQI) score, and AD burden score for adults (ADBSA; secondary end points), measured monthly for 3 months. An intention-to-treat sample was analyzed after adjusting baseline differences. RESULTS: On PO-SCORAD, improvement was higher in IH against placebo, but nonsignificant statistically (pmonth 1 = 0.433, pmonth 2 = 0.442, pmonth 3 = 0.229). Secondary outcomes were also nonsignificant - both DLQI and ADBSA (p > 0.05). Four adverse events (diarrhea, injury, common cold) were recorded. CONCLUSIONS: There was a small, but nonsignificant direction of effect towards homeopathy, which renders the trial inconclusive. A properly powered robust trial is indicated.

Feasibility of HPV self-sampling pathway in Kathmandu Valley, Nepal using a human-centred design approach.

Cervical cancer is preventable and curable yet causes almost 2000 deaths in Nepali women each year. The present study aims to explore the feasibility and acceptability of a self-sampling-based approach for cervical cancer screening in urban and peri-urban Nepal and develop pathways for self-sampling using a co-design methodology. An iterative design approach was applied. Semi-structured in-depth interviews were conducted with 30 healthy women and four women who had had a prior cancer diagnosis on topics which included: sexual and reproductive health knowledge and human papillomavirus (HPV); use of the internet/social media platforms; their views regarding acceptability and usability of the self-sampling kit and the proposed user journey. Data collection was done between December 2020 and January 2021. Seven medical experts were also interviewed to explore the current service configuration for cervical cancer screening in Nepal. Knowledge regarding HPV and its association with cervical cancer was absent for the majority of participants. Although 70% (n = 21/30) had purchased items online previously, there was a general lack of trust in online shopping. Half of the women (n = 17/30; 56.7%) expressed a willingness to self-sample and provided recommendations to improve the clarity of the instructions. The proposed user journey was considered feasible in the urban area. There is a clear unmet need for information about HPV and alternative cervical screening options in Nepal. An online pathway for self-sampling service delivery to urban women is feasible but will need to be optimally designed to address barriers such as confidence in self-sampling and trust in online purchasing.

Immunogenomic profiling and pathological response results from a clinical trial of docetaxel and carboplatin in triple-negative breast cancer.

PURPOSE: Patients with triple-negative breast cancer (TNBC) who do not achieve pathological complete response (pCR) following neoadjuvant chemotherapy have a high risk of recurrence and death. Molecular characterization may identify patients unlikely to achieve pCR. This neoadjuvant trial was conducted to determine the pCR rate with docetaxel and carboplatin and to identify molecular alterations and/or immune gene signatures predicting pCR. EXPERIMENTAL DESIGN: Patients with clinical stages II/III TNBC received 6 cycles of docetaxel and carboplatin. The primary objective was to determine if neoadjuvant docetaxel and carboplatin would increase the pCR rate in TNBC compared to historical expectations. We performed whole-exome sequencing (WES) and immune profiling on pre-treatment tumor samples to identify alterations that may predict pCR. Thirteen matching on-treatment samples were also analyzed to assess changes in molecular profiles. RESULTS: Fifty-eight of 127 (45.7%) patients achieved pCR. There was a non-significant trend toward higher mutation burden for patients with residual cancer burden (RCB) 0/I versus RCB II/III (median 80 versus 68 variants, p 0.88). TP53 was the most frequently mutated gene, observed in 85.7% of tumors. EGFR, RB1, RAD51AP2, SDK2, L1CAM, KPRP, PCDHA1, CACNA1S, CFAP58, COL22A1, and COL4A5 mutations were observed almost exclusively in pre-treatment samples from patients who achieved pCR. Seven mutations in PCDHA1 were observed in pre-treatment samples from patients who did not achieve pCR. Several immune gene signatures including IDO1, PD-L1, interferon gamma signaling, CTLA4, cytotoxicity, tumor inflammation signature, inflammatory chemokines, cytotoxic cells, lymphoid, PD-L2, exhausted CD8, Tregs, and immunoproteasome were upregulated in pre-treatment samples from patients who achieved pCR. CONCLUSION: Neoadjuvant docetaxel and carboplatin resulted in a pCR of 45.7%. WES and immune profiling differentiated patients with and without pCR. TRIAL REGISTRATION: Clinical trial information: NCT02124902, Registered 24 April 2014 & NCT02547987, Registered 10 September 2015.

Individualized Homeopathic Medicines in Stage I Essential Hypertension: A Double-Blind, Randomized, Placebo-Controlled Pilot Trial.

Objective: The present study assessed the feasibility of a definitive placebo-controlled trial for evaluating individualized homeopathy (IH) in stage I hypertension (HTN). Design: Double-blind, randomized (IH: 34, placebo: 34), placebo-controlled, parallel arms, pilot trial. Settings/Location: National Institute of Homoeopathy, India. Subjects: Patients suffering from stage I HTN. Interventions: IH and identical-looking placebo. Outcome measures: Feasibility issues, blood pressure (BP) and Measure Yourself Medical Outcome Profile-2 (MYMOP-2) were assessed for 6 months. Results: The recruitment and retention rates were 44.4% and 85.3%, respectively. Group differences were seemingly higher in the IH group than in the placebo group. Conclusions: Despite challenges in recruitment, an adequately powered efficacy trial appears feasible in the future.

Individualized Homeopathic Medicines in the Treatment of Generalized Anxiety Disorder: A Double-Blind, Randomized, Placebo-Controlled, Pilot Trial.

INTRODUCTION: Evidence favoring homeopathy in generalized anxiety disorder (GAD) remains scarce. The objective of this pilot trial was to test feasibility of a definitive trial in future. We also experimented whether individualized homeopathic medicines (IH) plus psychological counseling (PC) can produce significantly different effects beyond placebo plus PC in the treatment of GAD. METHODS: A double-blind, randomized, placebo-controlled, parallel arm, pilot trial was conducted on 62 GAD patients at the National Institute of Homoeopathy, India. GAD-7 questionnaire and Hamilton Anxiety Scale (HAM-A) were used as the primary and secondary outcomes, respectively, measured at baseline and 3 months. Patients received either IH plus PC (n = 31) or identical-looking placebo plus PC (n = 31). Intention-to-treat sample was analyzed to detect group differences using unpaired t tests. RESULTS: Recruitment and retention rates were 56 and 90%, respectively. Mean age was 31.5 years; 56.5% were male. GAD-7 reductions were non-significantly higher in IH than placebo (p = 0.122). Group differences on HAM-A favored IH significantly (p = 0.018). Effect sizes were small to medium. Calcarea carbonica was the most frequently indicated medicine. No serious adverse events happened. CONCLUSIONS: A small but positive direction of anxiolytic effect was observed favoring homeopathy over placebo. A definitive trial appeared feasible in future.

Individualized Homeopathic Medicines in Chronic Rhinosinusitis: Randomized, Double-Blind, Placebo-Controlled Trial.

BACKGROUND: Chronic rhinosinusitis (CRS) is a common disorder, with up to an estimated 134 million Indian sufferers, and having significant impact on quality of life (QOL) and health costs. Despite the evidence favoring homeopathy in CRS being inadequate, it is highly popular. This trial attempts to study the efficacy of individualized homeopathy (IH) medicines in comparison with placebo in patients with CRS. METHODS: A double-blind, randomized (1:1), placebo-controlled, preliminary trial (n = 62) was conducted at the National Institute of Homoeopathy, West Bengal, India. Primary outcome measure was the sino-nasal outcome test-20 (SNOT-20) questionnaire; secondary outcomes were the EQ-5D-5L questionnaire and EQ-5D-5L visual analog scale scores, and five numeric rating scales (0-10) assessing intensity of sneezing, rhinorrhea, post-nasal drip, facial pain/pressure, and disturbance in sense of smell, all measured at baseline and after the 2nd and 4th months of intervention. Group differences and effect sizes (Cohen's d) were calculated on the intention-to-treat sample. RESULTS: Groups were comparable at baseline. Attrition rate was 6.5% (IH: 1, Placebo: 3). Although improvements in both primary and secondary outcome measures were higher in the IH group than placebo, with small to medium effect sizes, the group differences were statistically non-significant (all p > 0.05, unpaired t-tests). Calcarea carbonica, Lycopodium clavatum, Sulphur, Natrum muriaticum and Pulsatilla nigricans were the most frequently prescribed medicines. No harmful or unintended effects, homeopathic aggravations or any serious adverse events were reported from either group. CONCLUSION: There was a small but non-significant direction of effect favoring homeopathy, which ultimately renders the trial as inconclusive. Rigorous trials and independent replications are recommended to arrive at a confirmatory conclusion. [Trial registration: CTRI/2018/03/012557; UTN: U1111-1210-7201].

Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2.

Angiotensin converting enzyme 2 (ACE2) (EC:3.4.17.23) is a transmembrane protein which is considered as a receptor for spike protein binding of novel coronavirus (SARS-CoV2). Since no specific medication is available to treat COVID-19, designing of new drug is important and essential. In this regard, in silico method plays an important role, as it is rapid and cost effective compared to the trial and error methods using experimental studies. Natural products are safe and easily available to treat coronavirus affected patients, in the present alarming situation. In this paper five phytochemicals, which belong to flavonoid and anthraquinone subclass, have been selected as small molecules in molecular docking study of spike protein of SARS-CoV2 with its human receptor ACE2 molecule. Their molecular binding sites on spike protein bound structure with its receptor have been analyzed. From this analysis, hesperidin, emodin and chrysin are selected as competent natural products from both Indian and Chinese medicinal plants, to treat COVID-19. Among them, the phytochemical hesperidin can bind with ACE2 protein and bound structure of ACE2 protein and spike protein of SARS-CoV2 noncompetitively. The binding sites of ACE2 protein for spike protein and hesperidin, are located in different parts of ACE2 protein. Ligand spike protein causes conformational change in three-dimensional structure of protein ACE2, which is confirmed by molecular docking and molecular dynamics studies. This compound modulates the binding energy of bound structure of ACE2 and spike protein. This result indicates that due to presence of hesperidin, the bound structure of ACE2 and spike protein fragment becomes unstable. As a result, this natural product can impart antiviral activity in SARS CoV2 infection. The antiviral activity of these five natural compounds are further experimentally validated with QSAR study.

Immunoinformatics Based Study of T Cell Epitopes in Zea m 1 Pollen Allergen.

Background and Objectives: Zea m 1 is a pollen allergen, which is present in maize, is accountable for a type I hypersensitivity reaction in all over the world. Several effective medications are available for the disorder with various side effects. Design and verification of a peptide-based vaccine is a state-of-art technology which is more cost effective than conventional drugs. Materials and Methods: Using immunoinformatic methods, the T cell epitopes from the whole structure of this allergenic protein can be predicted. Worldwide conserved region study among the other pollen allergens has been performed for T cell predicted epitopes by using a conservancy tool. This analysis will help to identify completely conserved HLA (human leukocyte antigen) binding epitopes. Lastly, molecular docking study and MHC-oligopeptide complex binding energy calculation data are applied to determine the interacting amino acids and the affinity of the epitopes to the class II MHCmolecule. Results: The study of criteria-based analysis predicts the presence of two epitopes YVADDGDIV and WRMDTAKAL on this pollen allergen. Conclusions: The T cell epitopes identified in this study provide insight into a peptide-based vaccine for a type I hypersensitivity reaction induced by Zea m 1 grass pollen allergenic protein.

Effects of omega-3 polyunsaturated fatty-acid supplementation on neuropathic pain symptoms and sphingosine levels in Mexican-Americans with type 2 diabetes.

PURPOSE: To determine whether dietary supplementation with omega-3 polyunsaturated fatty acids (PUFAs) reduces neuropathic pain symptoms in Mexican-Americans with type 2 diabetes. METHODS: Forty volunteers with type 2 diabetes enrolled in the "En Balance-PLUS" program, which provided weekly nutrition-diabetes education and daily supplementation with 1,000 mg docosahexaenoic acid (DHA)-200 mg eicosapentaenoic acid over 3 months. The study assessed self-reported neuropathic pain symptoms pre/postintervention using the short-form McGill Pain Questionnaire (SF-MPQ), monitored clinical laboratory values at baseline and 3 months, and performed baseline and 3-month metabolomic analysis of plasma samples. RESULTS: A total of 26 participants self-reported neuropathic pain symptoms at baseline. After 3 months of omega-3 PUFA supplementation, participants reported significant improvement in SF-MPQ scores (sensory, affective, and visual analogue scale; P<0.001, P=0.012, and P<0.001, respectively). Untargeted metabolomic analysis revealed that participants in the moderate-high SF-MPQ group had the highest relative plasma sphingosine levels at baseline compared to the low SF-MPQ group (P=0.0127) and the nonpain group (P=0.0444). Omega-3 PUFA supplementation increased plasma DHA and reduced plasma sphingosine levels in participants reporting neuropathic pain symptoms (P<0.001 and P<0.001, respectively). Increased plasma DHA levels significantly correlated with improved SF-MPQ sensory scores (r=0.425, P=0.030). Improved SF-MPQ scores, however, did not correlate with clinical/laboratory parameters. CONCLUSION: The data suggest that omega-3 PUFAs dietary supplementation may reduce neuropathic pain symptoms in individuals with type 2 diabetes and correlates with sphingosine levels in the plasma.

Glucocorticoids Induce Stress Oncoproteins Associated with Therapy-Resistance in African American and European American Prostate Cancer Cells.

Glucocorticoid receptor (GR) is emerging as a key driver of prostate cancer (PCa) progression and therapy resistance in the absence of androgen receptor (AR) signaling. Acting as a bypass mechanism, GR activates AR-regulated genes, although GR-target genes contributing to PCa therapy resistance remain to be identified. Emerging evidence also shows that African American (AA) men, who disproportionately develop aggressive PCa, have hypersensitive GR signaling linked to cumulative stressful life events. Using racially diverse PCa cell lines (MDA-PCa-2b, 22Rv1, PC3, and DU145) we examined the effects of glucocorticoids on the expression of two stress oncoproteins associated with PCa therapy resistance, Clusterin (CLU) and Lens Epithelium-Derived Growth Factor p75 (LEDGF/p75). We observed that glucocorticoids upregulated LEDGF/p75 and CLU in PCa cells. Blockade of GR activation abolished this upregulation. We also detected increased GR transcript expression in AA PCa tissues, compared to European American (EA) tissues, using Oncomine microarray datasets. These results demonstrate that glucocorticoids upregulate the therapy resistance-associated oncoproteins LEDGF/p75 and CLU, and suggest that this effect may be enhanced in AA PCa. This study provides an initial framework for understanding the contribution of glucocorticoid signaling to PCa health disparities.

RNA sequencing reveals upregulation of a transcriptomic program associated with stemness in metastatic prostate cancer cells selected for taxane resistance.

Patients with metastatic castration-resistant prostate cancer (mCRPC) develop resistance to conventional therapies including docetaxel (DTX). Identifying molecular pathways underlying DTX resistance is critical for developing novel combinatorial therapies to prevent or reverse this resistance. To identify transcriptomic signatures associated with acquisition of chemoresistance we profiled gene expression in DTX-sensitive and -resistant mCRPC cells using RNA sequencing (RNA-seq). PC3 and DU145 cells were selected for DTX resistance and this phenotype was validated by immunoblotting using DTX resistance markers (e.g. clusterin, ABCB1/P-gp, and LEDGF/p75). Overlapping genes differentially regulated in the DTX-sensitive and -resistant cells were ranked by Gene Set Enrichment Analysis (GSEA) and validated to correlate transcript with protein expression. GSEA revealed that genes associated with cancer stem cells (CSC) (e.g., NES, TSPAN8, DPPP, DNAJC12, and MYC) were highly ranked and comprised 70% of the top 25 genes differentially upregulated in the DTX-resistant cells. Established markers of epithelial-to-mesenchymal transition (EMT) and CSCs were used to evaluate the stemness of adherent DTX-resistant cells (2D cultures) and tumorspheres (3D cultures). Increased formation and frequency of cells expressing CSC markers were detected in DTX-resistant cells. DU145-DR cells showed a 2-fold increase in tumorsphere formation and increased DTX resistance compared to DU145-DR 2D cultures. These results demonstrate the induction of a transcriptomic program associated with stemness in mCRPC cells selected for DTX resistance, and strengthen the emerging body of evidence implicating CSCs in this process. In addition, they provide additional candidate genes and molecular pathways for potential therapeutic targeting to overcome DTX resistance.

The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers.

BACKGROUND: Elevated PD-L1 expression on tumor cells, a context associated with an adaptive immune response, has been linked to the total burden of copy number variants (CNVs) in aneuploid tumors, to microsatellite instability (MSI), and to specific genomic driver lesions, including loss of PTEN, MYC amplification, and activating mutations in driver oncogenes such as KRAS and PIK3CA. Triple-negative breast cancers (TNBCs) typically have high levels of CNVs and diverse driver lesions in their genomes. Thus, there is significant interest in exploiting genomic data to develop predictive immunotherapy biomarkers for patients with TNBC. METHODS: Whole tissue samples from 55 resected TNBCs were screened by immunohistochemistry (IHC) for PD-1 and PD-L1 by using validated antibodies and established scoring methods for staining of tumor and non-tumor cells. In parallel, we interrogated biopsies from each resection with DNA content flow cytometry and sorted the nuclei of diploid, tetraploid, and aneuploid cell populations. CNVs were mapped with CNV oligonucleotide arrays by using purified (>95%) tumor populations. We generated whole exome data for 12 sorted tumor samples to increase the resolution within loci of interest and to incorporate somatic mutations into our genomic signatures. RESULTS AND CONCLUSIONS: PD-L1 staining was detected on tumor cells in 29 out of 54 (54%) evaluable cases and was associated with increased overall survival (P = 0.0024). High levels of PD-1 and PD-L1 (IHC ≥4) were present in 11 out of 54 (20%) and 20 out of 54 (37%) cases with staining of PD-L1 primarily on tumor cells for 17 out of 20 (85%) cases. The latter included tumors with both high (>50) and low (<20) numbers of CNVs. Notably, homozygous deletion of PTEN (n = 6) or activating mutation in PIK3CA (n = 1) was not associated with increased expression of either immune checkpoint activator in TNBC. In contrast, two treatment-naïve cases with EGFR driver amplicons had high PD-L1 tumor staining. High mutational load and predicted neoepitopes were observed in MSI+ and high CNV burden TNBCs but were not associated with high PD-L1 expression on tumor cells. Our results challenge current models of genomic-based immunotherapy signatures yet suggest that discrete genomic lesions may complement existing biomarkers to advance immune checkpoint therapies for patients with TNBC.

The 22Rv1 prostate cancer cell line carries mixed genetic ancestry: Implications for prostate cancer health disparities research using pre-clinical models.

BACKGROUND: Understanding how biological factors contribute to prostate cancer (PCa) health disparities requires mechanistic functional analysis of specific genes or pathways in pre-clinical cellular and animal models of this malignancy. The 22Rv1 human prostatic carcinoma cell line was originally derived from the parental CWR22R cell line. Although 22Rv1 has been well characterized and used in numerous mechanistic studies, no racial identifier has ever been disclosed for this cell line. In accordance with the need for racial diversity in cancer biospecimens and recent guidelines by the NIH on authentication of key biological resources, we sought to determine the ancestry of 22RV1 and authenticate previously reported racial identifications for four other PCa cell lines. METHODS: We used 29 established Ancestry Informative Marker (AIM) single nucleotide polymorphisms (SNPs) to conduct DNA ancestry analysis and assign ancestral proportions to a panel of five PCa cell lines that included 22Rv1, PC3, DU145, MDA-PCa-2b, and RC-77T/E. RESULTS: We found that 22Rv1 carries mixed genetic ancestry. The main ancestry proportions for this cell line were 0.41 West African (AFR) and 0.42 European (EUR). In addition, we verified the previously reported racial identifications for PC3 (0.73 EUR), DU145 (0.63 EUR), MDA-PCa-2b (0.73 AFR), and RC-77T/E (0.74 AFR) cell lines. CONCLUSIONS: Considering the mortality disparities associated with PCa, which disproportionately affect African American men, there remains a burden on the scientific community to diversify the availability of biospecimens, including cell lines, for mechanistic studies on potential biological mediators of these disparities. This study is beneficial by identifying another PCa cell line that carries substantial AFR ancestry. This finding may also open the door to new perspectives on previously published studies using this cell line.